Abstract:
Genome synthesis has become an important tool in many fields of recombinant DNA technology
including vaccine development, gene therapy and molecular engineering. There
had been a number of researches that investigated the function of genes in a sequence
and how to synthesize genome sequence according to user specification. The purpose of
this study is to find a genome sequence which provides maximum amount of flexibility
and independence to biologists to run experiment with the sequence. Restriction enzymes
are reagents widely used by molecular biologists for genetic manipulation and analysis.
The decision version of Unique Restriction Site Placement Problem (URSPP) has been
proved to be NP complete. Since URSPP is a multi-objective optimization problem and
multi-objective optimization often shows good performance through elitist approach, our
target is to introduce elitism in different meta-heuristic strategies to solve URSPP. Additionally,
we change one of the objectives of URSPP to make the problem biologically
more interesting and meaningful. We carry out extensive experiments considering different
clinically important viruses as well as large viral sequences considering existing
meta-heuristic algorithms in the literature as well as our newly developed algorithms.
Our experimental results show that our approaches give better results than traditional
meta-heuristics. As a result, we provide a software tool according to our approach which
would be helpful for genome synthesis from biological viewpoint.
